LIFE SCIENCE

Deciphering the complex genome and decoding the “Chinese core” of naked oats


Naked oats (quinoa) Courtesy of respondents

As a worldwide cultivated crop distributed in 42 countries and regions on five continents, oats are divided into two types: peeled oats and naked oats. Among them, naked oats originated independently in China and are widely cultivated, and are affectionately known as “yarrow” by the Chinese people.

On July 18, Nature-Heredity published a high-quality genomic atlas of hexaploid naked oats online, opening the door to the naked oat genome.

“This research was all done by Chinese himself. In-depth study of China’s unique oat germplasm resources is to firmly hold the germplasm resources in our own hands, so that oat varieties can be loaded with more ‘Chinese cores’. Ren Changzhong, chief scientist of the national oat and buckwheat industry technology system and researcher of the Baicheng Academy of Agricultural Sciences in Jilin Province, who led the study, said.

The reviewers argue that “this genome is one of the most complex of all species sequenced to date” and “represents a significant advance in plant genomics, particularly cereal genomics.”

Race against your peers all over the world

As the best full-price nutritional food in cereals, oats are rich in protein, unsaturated fatty acids and soluble dietary fiber, which can meet people’s requirements for both dietary nutrition and health care.

Peel oat grains are in the grain type, and the grain is closely linked to the seeds and is difficult to break off after maturity; The bare oat grain is of the bare grain type, and the barnyard leather is particularly soft and naturally separated from the seeds after maturity. Compared with peeled oats, the processing process of naked oats is simpler, with higher protein and crude fat content, and the amino acid composition is more balanced, which is of great research value.

At present, the cultivated species in various countries in the world are mainly peeled oats. China mainly grows naked oats, the main production areas are concentrated in Inner Mongolia, Hebei, Shanxi, Qinghai, Gansu, Jilin, Shaanxi, Ningxia and Xinjiang and other places, Yun, Gui, Sichuan, Tibet also have small areas of planting. Among them, Inner Mongolia has the largest planting area, reaching more than 4 million mu. In recent years, China’s oat industry is developing rapidly at a rate of more than 20% of annual output value.

“The skin nude trait of oat grains is one of the important domestication traits.” Peng Yuanying, the first author of the paper and a professor at Sichuan Agricultural University, told China Science Daily that oats, as a hexarium crop, have significant advantages in biomass, vitality and adaptability to environmental changes, and can play a unique role in coping with food security challenges.

Ren Changzhong, corresponding author of the paper, believes that “China, as the origin and cultivation center of naked oats, has a unique competitive advantage of germplasm chips. The sequencing of the naked oat genome originating from China should be completed by the Chinese, which is of great significance for improving the competitiveness of the domestic oat industry and ensuring food security. ”

However, oats are hexaploid crops with large genomes and high repetitive sequence content, which makes its genome sequencing and assembly a world problem.

“Ten years ago, foreign counterparts began to do genome sequencing research on peeled oats, but due to the difficulty, there was no result. Later, all of their counterparts studying oats abroad, including the United Kingdom, Germany, the United States, Australia, Sweden, and Canada, joined forces with scientists who had deciphered the genome maps of barley and wheat to overcome the oat genome problem. Peng Yuanying said.

In China, the oat research team led by Ren Changzhong has been engaged in oat research for a long time and has accumulated rich experience. Especially in the past 20 years, Peng Yuanying and other teams have been focusing on the origin and evolution of oat species, laying a good foundation for the sequencing of the genome of hexaploid oats.

In 2018, with the support of the National Oat And Buckwheat Industry Technology System and the National Natural Science Foundation of China, the joint research team of Oats of Sichuan Agricultural University and Baicheng Academy of Agricultural Sciences of Jilin Province cooperated with the Institute of Genetics and Development of the Chinese Academy of Sciences, Sichuan University, Xichang College, Chinese Academy of Agricultural Sciences and Wuhan Hope Group Biotechnology Co., Ltd. to officially launch the sequencing of naked oat genomes.

The oat research team, which is entirely composed of Chinese scientists, is facing a joint team of oat researchers from other countries. “This adds a sense of urgency to our work on bare oats.” Peng Yuanying said.

Decipher complex genomes

Existing cultivated oats have naturally hybridized and doubled over a long evolutionary process, forming tetraploidy from diploid and eventually multiplication into hexaploids containing three genomes of A, C, and D. Thus, the naked oat genome consists of about 11 billion base pairs distributed in 21 pairs of chromosomes in 3 subgenomes of the nucleus. Its genome is large and complex, about 40 times the size of the rice genome, and about 87% of the genomic DNA is a repetitive sequence, making it very difficult to sequence and assemble its genome.

So, how to find another way to catch up with the foreign team that has gathered the world’s strongest scientific research forces?

Peng Yuanying told reporters that in view of the assembly problems caused by the subgenome composition of hexaploid oats and their high repetitive sequence content, they chose a high-precision ultra-long sequencing technology, and used the nearly 20 years of oat species research experience to select the most likely tetraploid and diploid ancestors of cultivated oats to build their genomes together as a reference, so that the genome assembly of hexaploid cultivated oats was successfully completed.

The results of this publication are based on the local oat varieties “three-thirds” of the origin center of naked oats in China. Through the study of “three-thirds”, the molecular map of 21 pairs of chromosomes in the oat genome was mapped, and 120,000 protein-coding genes were annotated, and the high-quality reference genome of naked oats was obtained.

After the paper was submitted to the journal Nature, it received high praise. One reviewer said the assembly and annotation of the genome, as well as the accompanying genome and resequencing resources, were of high quality. The “three-thirds” genome is novel enough because it is quite unique in its genetic position.

Another reviewer said the data and analysis provided by this work is highly novel, providing new insights into the genomic evolution of large multiploid genomes.

A month later, the genome atlas of peel oats jointly completed by foreign counterparts was also submitted to Nature.

Ren Changzhong said: “Our Chinese team withstood the pressure and preemptively completed the research results. ”

Oat research enters the genomic era

After obtaining a high-quality genome map, what Peng Yuanying wanted to know most was the evolutionary process of oats. “Where oats evolved has always been a scientific mystery.” This is also one of the topics she has studied for many years.

They selected species that represent all the existing genomic types of Oats, combined with other closely related genera species such as rice and wheat, and analyzed the evolutionary status of oats in major cereal crops at the genome-wide level, as well as the origin and multiplication history of cultivated oats.

It was found that the differentiation between the oat family and the wheat tribe occurred after the formation of the rice family, and the relationship between the oat family and the multi-flowered ryegrass was closer than that between the oat family and the wheat family. Oat species emerged about 8 million years ago. About 500,000 years ago, in the Paleolithic age of mankind, hexaploid cultivation of oats was formed by the hybridization of AA genome diploid and CCDD genome tetraploidy.

“An in-depth understanding of the evolutionary history of oats will greatly facilitate osmotic breeding and transfer beneficial traits from the closest existing wild relatives of oats to cultivated oats, which will strongly promote the selection and breeding of excellent varieties of high-quality oats.” Peng Yuanying said that with the genome map, the breeding and genetic research of naked oats in China will enter the fast lane.

“Just like cracking the genetic code of other crops, we can later cultivate naked oats with specific traits and functions based on genetic information, such as improving the disease resistance of varieties; Control seed size and increase yield; Or make it more β-dextran, helping eaters effectively control cholesterol and diabetes through dietary fiber intake. Ren Changzhong said.

Oats are threatened by disease during growth, the most serious of which is coronary rust. The team identified 1269 resistance genes in three subgenomes of hexaploid oats. Most resistance genes appear in clusters at the ends of chromosomes and are co-localized with known segments of crown rust genes in oats, suggesting that the oat reference genome constructed in this study can provide an effective reference for the localization and cloning of oat disease resistance genes.

They also performed genome-wide association analysis of 659 cultivars of different origins and found a candidate gene that controls the nude traits of oat grain skin.

The research team believes that the construction of the oat reference genome as the first step in the genomic era of oat research will make it possible to select and breed oats throughout the genome and precision breeding. “We can now begin to think about how modern breeding strategies, such as genome editing, can be used to further refine and develop specific oat varieties to meet the growing global demand for this healthy food and quality forage.”

Next, the team will also combine the original research advantages, and further carry out research work on the origin, domestication and exploration and utilization of excellent genetic resources of oats on the existing basis, hoping that the research results will further promote the application of basic research and breeding of oats. (Source: China Science Daily, Li Chen, Zhang Qingdan, Yang Wen)

Related paper information:https://doi.org/10.1038/s41588-022-01127-7



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